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Genes 2015, 6(3), 841-857; doi:10.3390/genes6030841

Ecology and Evolution of the Human Microbiota: Fire, Farming and Antibiotics

Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
Author to whom correspondence should be addressed.
Academic Editors: Jonathan Iredell and Sally Partridge
Received: 17 July 2015 / Revised: 26 August 2015 / Accepted: 31 August 2015 / Published: 8 September 2015
(This article belongs to the Special Issue Antibiotic Resistance: Mobility and Microbiomes)
View Full-Text   |   Download PDF [791 KB, uploaded 8 September 2015]   |  


Human activities significantly affect all ecosystems on the planet, including the assemblages that comprise our own microbiota. Over the last five million years, various evolutionary and ecological drivers have altered the composition of the human microbiota, including the use of fire, the invention of agriculture, and the increasing availability of processed foods after the Industrial Revolution. However, no factor has had a faster or more direct effect than antimicrobial agents. Biocides, disinfectants and antibiotics select for individual cells that carry resistance genes, immediately reducing both overall microbial diversity and within-species genetic diversity. Treated individuals may never recover their original diversity, and repeated treatments lead to a series of genetic bottlenecks. The sequential introduction of diverse antimicrobial agents has selected for increasingly complex DNA elements that carry multiple resistance genes, and has fostered their spread through the human microbiota. Practices that interfere with microbial colonization, such as sanitation, Caesarian births and bottle-feeding, exacerbate the effects of antimicrobials, generating species-poor and less resilient microbial assemblages in the developed world. More and more evidence is accumulating that these perturbations to our internal ecosystems lie at the heart of many diseases whose frequency has shown a dramatic increase over the last half century. View Full-Text
Keywords: integron; evolution; mercury; disinfectant; resistance; antibiotic; Anthropocene; dysbiosis integron; evolution; mercury; disinfectant; resistance; antibiotic; Anthropocene; dysbiosis

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Gillings, M.R.; Paulsen, I.T.; Tetu, S.G. Ecology and Evolution of the Human Microbiota: Fire, Farming and Antibiotics. Genes 2015, 6, 841-857.

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